The northern quahog, Mercenaria mercenaria (= hard clam) is an important aquaculture species on the U.S. east coast and shares a partially sympatric distribution with a sister species Mercenaria campechiensis which is endemic to the mid-Atlantic coast from the Chesapeake Bay to Florida and the Gulf of Mexico. These two species are morphologically similar, and their identification is laborious and challenging. To support aquaculture breeding and restoration activities, it is essential to develop an accurate and easy method to identify the two Mercenaria species. In the present study, high-melting resolution analysis was applied to identify these two Mercenaria species and their hybrids using three genes of cytochrome oxidase subunit 1 (CO1), mitochondrial large ribosomal subunit (16S rRNA), and internal transcribed spacer 1 (ITS1). The temperature melting points (T_m) of CO1, 16S rRNA, and ITS1 were significantly different between the two Mercenaria species and could be used to distinguish M. mercenaria and M. campechiensis. By use of the melting T_m of CO1, 16S rRNA, and ITS1, a discriminant function equation was established to effectively eliminate the impacts of intraspecific sequence variations on species identification. Compared with their true species classification, the accuracy of the predicted classification of each sample was 100% based on the discriminant function equation. Furthermore, a linear discriminant analysis model was used for cross-validation and the mean classification success was 100% with no observed erroneous classification. Moreover, the interspecific hybrids of M. mercenaria and M. campechiensis were verified by the melting curve of nuclear DNA marker ITS1, and their maternity was further clarified by mitochondrial DNA markers CO1 and 16S rRNA. The methodology developed in this study would be useful as a rapid and accurate tool to support Mercenaria aquaculture, breeding, and restoration.